@article{Larsen2017,
	doi = {10.1088/1361-648x/aa680e},
	url = {https://doi.org/10.1088/1361-648x/aa680e},
	year = 2017,
	month = {jun},
	publisher = {{IOP} Publishing},
	volume = {29},
	number = {27},
	pages = {273002},
	author = {Ask Hjorth Larsen and Jens J{\o}rgen Mortensen and Jakob Blomqvist and Ivano E Castelli and Rune Christensen and Marcin Du{\l}ak and Jesper Friis and Michael N Groves and Bj{\o}rk Hammer and Cory Hargus and Eric D Hermes and Paul C Jennings and Peter Bjerre Jensen and James Kermode and John R Kitchin and Esben Leonhard Kolsbjerg and Joseph Kubal and Kristen Kaasbjerg and Steen Lysgaard and J{\'{o}}n Bergmann Maronsson and Tristan Maxson and Thomas Olsen and Lars Pastewka and Andrew Peterson and Carsten Rostgaard and Jakob Schi{\o}tz and Ole Schütt and Mikkel Strange and Kristian S Thygesen and Tejs Vegge and Lasse Vilhelmsen and Michael Walter and Zhenhua Zeng and Karsten W Jacobsen},
	title = {The atomic simulation environment{\textemdash}a Python library for working with atoms},
	journal = {Journal of Physics: Condensed Matter},
	abstract = {The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.}
}

@article{AtomMan,
  author = {Lucas Hale},
  year = {2022},
  url = {https://github.com/usnistgov/atomman}
}


@ARTICLE{Stukowski2009,
  title     = "Visualization and analysis of atomistic simulation data with
               {OVITO--the} Open Visualization Tool",
  author    = "Stukowski, Alexander",
  abstract  = "The Open Visualization Tool (OVITO) is a new 3D visualization
               software designed for post-processing atomistic data obtained
               from molecular dynamics or Monte Carlo simulations. Unique
               analysis, editing and animations functions are integrated into
               its easy-to-use graphical user interface. The software is
               written in object-oriented C++, controllable via Python scripts
               and easily extendable through a plug-in interface. It is
               distributed as open-source software and can be downloaded from
               the website http://ovito.sourceforge.net/.",
  journal   = "Modell. Simul. Mater. Sci. Eng.",
  publisher = "IOP Publishing",
  volume    =  18,
  number    =  1,
  pages     = "015012",
  month     =  dec,
  year      =  2009,
  language  = "en",
  issn      = "0965-0393",
  doi       = "10.1088/0965-0393/18/1/015012"
}


@ARTICLE{Bernstein2009,
  title    = "Hybrid atomistic simulation methods for materials systems",
  author   = "Bernstein, Noam and Kermode, J R and Cs{\'a}nyi, G",
  abstract = "N 1 , JR 2,3 and G Csanyi CB2 1PZ, UK E-mail: noam. @nrl. navy
              review recent progress in the methodology of /classical (QM",
  journal  = "Rep. Prog. Phys.",
  volume   =  72,
  number   =  2,
  pages    = "026501",
  year     =  2009,
  issn     = "0034-4885",
  doi      = "10.1088/0034-4885/72/2/026501"
}

@ARTICLE{Musil2019,
  title    = "Fast and Accurate Uncertainty Estimation in Chemical Machine
              Learning",
  author   = "Musil, F{\'e}lix and Willatt, Michael J and Langovoy, Mikhail A
              and Ceriotti, Michele",
  abstract = "We present a scheme to obtain an inexpensive and reliable
              estimate of the uncertainty associated with the predictions of a
              machine-learning model of atomic and molecular properties. The
              scheme is based on resampling, with multiple models being
              generated based on subsampling of the same training data. The
              accuracy of the uncertainty prediction can be benchmarked by
              maximum likelihood estimation, which can also be used to correct
              for correlations between resampled models and to improve the
              performance of the uncertainty estimation by a cross-validation
              procedure. In the case of sparse Gaussian Process Regression
              models, this resampled estimator can be evaluated at negligible
              cost. We demonstrate the reliability of these estimates for the
              prediction of molecular and materials energetics and for the
              estimation of nuclear chemical shieldings in molecular crystals.
              Extension to estimate the uncertainty in energy differences,
              forces, or other correlated predictions is straightforward. This
              method can be easily applied to other machine-learning schemes
              and will be beneficial to make data-driven predictions more
              reliable and to facilitate training-set optimization and
              active-learning strategies.",
  journal  = "J. Chem. Theory Comput.",
  volume   =  15,
  number   =  2,
  pages    = "906--915",
  month    =  feb,
  year     =  2019,
  language = "en",
  issn     = "1549-9618, 1549-9626",
  pmid     = "30605342",
  doi      = "10.1021/acs.jctc.8b00959"
}


@ARTICLE{Golebiowski2018,
  title     = "Multiscale simulations of critical interfacial failure in carbon
               nanotube-polymer composites",
  author    = "Go{\l}{\k e}biowski, Jacek R and Kermode, James R and Mostofi,
               Arash A and Haynes, Peter D",
  abstract  = "Computational investigation of interfacial failure in composite
               materials is challenging because it is inherently multi-scale:
               the bond-breaking processes that occur at the covalently bonded
               interface and initiate failure involve quantum mechanical
               phenomena, yet the mechanisms by which external stresses are
               transferred through the matrix occur on length and time scales
               far in excess of anything that can be simulated quantum
               mechanically. In this work, we demonstrate and validate an
               adaptive quantum mechanics (QM)/molecular mechanics simulation
               method that can be used to address these issues and apply it to
               study critical failure at a covalently bonded carbon nanotube
               (CNT)-polymer interface. In this hybrid approach, the majority
               of the system is simulated with a classical forcefield, while
               areas of particular interest are identified on-the-fly and
               atomic forces in those regions are updated based on QM
               calculations. We demonstrate that the hybrid method results are
               in excellent agreement with fully QM benchmark simulations and
               offers qualitative insights missing from classical simulations.
               We use the hybrid approach to show how the chemical structure at
               the CNT-polymer interface determines its strength, and we
               propose candidate chemistries to guide further experimental work
               in this area.",
  journal   = "J. Chem. Phys.",
  publisher = "American Institute of Physics",
  volume    =  149,
  number    =  22,
  pages     = "224102",
  month     =  dec,
  year      =  2018,
  issn      = "0021-9606",
  doi       = "10.1063/1.5035508"
}


@ARTICLE{Golebiowski2020,
  title    = "Atomistic {QM/MM} simulations of the strength of covalent
              interfaces in carbon nanotube-polymer composites",
  author   = "Go{\l}{\k e}biowski, Jacek R and Kermode, James R and Haynes,
              Peter D and Mostofi, Arash A",
  abstract = "We investigate the failure of carbon-nanotube/polymer composites
              by using a recently-developed hybrid
              quantum-mechanical/molecular-mechanical (QM/MM) approach to
              simulate nanotube pull-out from a cross-linked polyethene matrix.
              Our study focuses on the strength and failure modes of
              covalently-bonded nanotube-polymer interfaces based on amine,
              carbene and carboxyl functional groups and a [2+1] cycloaddition.
              We find that the choice of the functional group linking the
              polymer matrix to the nanotube determines the effective strength
              of the interface, which can be increased by up to 50\% (up to the
              limit dictated by the strength of the polymer backbone itself) by
              choosing groups with higher interfacial binding energy. We rank
              the functional groups presented in this work based on the
              strength of the resulting interface and suggest broad guidelines
              for the rational design of nanotube functionalisation for
              nanotube-polymer composites.",
  journal  = "Phys. Chem. Chem. Phys.",
  month    =  may,
  year     =  2020,
  language = "en",
  issn     = "1463-9076, 1463-9084",
  pmid     = "32421117",
  doi      = "10.1039/d0cp01841d"
}


@article{Grigorev2020,
  title = {Hybrid quantum/classical study of hydrogen-decorated screw dislocations in tungsten: Ultrafast pipe diffusion, core reconstruction, and effects on glide mechanism},
  author = {Grigorev, Petr and Swinburne, Thomas D. and Kermode, James R.},
  journal = {Phys. Rev. Materials},
  volume = {4},
  issue = {2},
  pages = {023601},
  numpages = {10},
  year = {2020},
  month = {Feb},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevMaterials.4.023601},
  url = {https://link.aps.org/doi/10.1103/PhysRevMaterials.4.023601}
}

@article{Grigorev2023,
title = {Calculation of dislocation binding to helium-vacancy defects in tungsten using hybrid ab initio-machine learning methods},
journal = {Acta Materialia},
volume = {247},
pages = {118734},
year = {2023},
issn = {1359-6454},
doi = {10.1016/j.actamat.2023.118734},
author = {Petr Grigorev and Alexandra M. Goryaeva and Mihai-Cosmin Marinica and James R. Kermode and Thomas D. Swinburne},
keywords = {Plasticity, Dislocations, Tungsten, Helium, Segregation, Density functional theory, QM/MM, Machine learning},
abstract = {Calculations of dislocation-defect interactions are essential to model metallic strength, but the required system sizes are at or beyond ab initio limits. Current estimates thus have extrapolation or finite size errors that are very challenging to quantify. Hybrid methods offer a solution, embedding small ab initio simulations in an empirical medium. However, current implementations can only match mild elastic deformations at the ab initio boundary. We describe a robust method to employ linear-in-descriptor machine learning potentials as a highly flexible embedding medium, precisely matching dislocation migration pathways whilst keeping at least the elastic properties constant. This advanced coupling allows dislocations to cross the ab initio boundary in fully three dimensional defect geometries. Investigating helium and vacancy segregation to edge and screw dislocations in tungsten, we find long-range relaxations qualitatively change impurity-induced core reconstructions compared to those in short periodic supercells, even when multiple helium atoms are present. We also show that helium-vacancy complexes, considered to be the dominant configuration at low temperatures, have only a very weak binding to screw dislocations. These results are discussed in the context of recent experimental and theoretical studies. More generally, our approach opens a vast range of mechanisms to ab initio investigation and provides new reference data to both validate and improve interatomic potentials.},
}

@article{Pastewka2010,
  doi = {10.1007/s11249-009-9566-8},
  year = {2010},
  month = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {39},
  number = {1},
  pages = {49--61},
  author = {Lars Pastewka and Stefan Moser and Michael Moseler},
  title = {Atomistic Insights into the Running-in,  Lubrication,  and Failure of Hydrogenated Diamond-Like Carbon Coatings},
  journal = {Tribology Letters}
}

@article{StillingerWeber1985,
  title={Computer simulation of local order in condensed phases of silicon},
  author={Stillinger, Frank H and Weber, Thomas A},
  journal={Phys. Rev. B},
  volume={31},
  number={8},
  pages={5262},
  year={1985},
  publisher={APS},
  doi={10.1103/PhysRevB.31.5262}
}

@article{Kumagai2007,
  title={Development of bond-order potentials that can reproduce the elastic constants and melting point of silicon for classical molecular dynamics simulation},
  author={Kumagai, T and Izumi, S and Hara, S and Sakai, S},
  journal={Computational materials science},
  volume={39},
  number={2},
  pages={457--464},
  year={2007},
  publisher={Elsevier},
  doi={10.1016/j.commatsci.2006.07.013}
}

@article{Tersoff1986,
	title = {New Empirical Model for the Structural Properties of Silicon},
	volume = {56},
	issn = {0031-9007},
	number = {6},
	journal = {Phys. Rev. Lett.},
	author = {Tersoff, J},
	year = {1986},
	pages = {632--635},
	doi = {10.1103/PhysRevLett.56.632}
}

@article{Tersoff1989,
  title={Modeling solid-state chemistry: Interatomic potentials for multicomponent systems},
  volume = {39},
  number = {8},
  author={Tersoff, J},
  journal={Phys. Rev. B},
  pages={5566(R)},
  year={1989},
  publisher={APS},
  doi={10.1103/PhysRevB.39.5566}
}

@article{Brenner1990,
	title = {Empirical potential for hydrocarbons for use in simulating chemical vapor deposition of diamond films},
	volume = {42},
	number = {15},
	journal = {Phys. Rev. B},
	author = {Brenner, Donald W.},
	year = {1990},
	pages = {9458--9471},
	file = {Brenner 1990 - Empirical potential for hydrocarbons for use in simulating chemical vapor deposition of diamond films:C\:\\Users\\Lars Pastewka\\Zotero\\storage\\Q32QX6R5\\Brenner 1990 - Empirical potential for hydrocarbons for use in simulating chemical vapor deposition of diamond films.pdf:application/pdf},
	optdoi = {10.1103/PhysRevB.42.9458},
}

@article{BKS1990,
  title={Force fields for silicas and aluminophosphates based on ab initio calculations},
  author={Van Beest, BWH and Kramer, Gert Jan and Van Santen, RA},
  journal={Phys. Rev. Lett.},
  volume={64},
  number={16},
  pages={1955},
  year={1990},
  publisher={APS},
  doi={10.1103/PhysRevLett.64.1955}
}

@article{Lennard1931,
  title={Cohesion},
  author={Lennard-Jones, John E},
  journal={Proc. Phys. Soc.},
  volume={43},
  number={5},
  pages={461-482},
  year={1931},
  publisher={IOP Publishing},
  doi={10.1088/0959-5309/43/5/301}
}

@ARTICLE{Sih1965,
  title   = "On cracks in rectilinearly anisotropic bodies",
  author  = "Sih, G C and Paris, P C and Irwin, G R",
  journal = "Int. J. Fract. Mech.",
  volume  =  1,
  number  =  3,
  pages   = "189--203",
  month   =  sep,
  year    =  1965,
  issn    = "0020-7268",
  doi     = "10.1007/BF00186854"
}

@ARTICLE{Sinclair1975,
  title   = "The Influence of the Interatomic Force Law and of Kinks on the
             Propagation of Brittle Cracks",
  author  = "Sinclair, J E",
  journal = "Philos. Mag.",
  volume  =  31,
  pages   = "647--671",
  year    =  1975,
  issn    = "1478-6435",
  doi     = "10.1080/14786437508226544"
}

@ARTICLE{Kermode2015,
  title     = "Low Speed Crack Propagation via Kink Formation and Advance on
               the Silicon (110) Cleavage Plane",
  author    = "Kermode, James R and Gleizer, Anna and Kovel, Guy and Pastewka,
               Lars and Cs{\'a}nyi, G{\'a}bor and Sherman, Dov and De Vita,
               Alessandro",
  journal   = "Phys. Rev. Lett.",
  publisher = "American Physical Society",
  volume    =  115,
  number    =  13,
  pages     = "135501",
  month     =  sep,
  year      =  2015,
  issn      = "0031-9007",
  doi       = "10.1103/PhysRevLett.115.135501"
}


@ARTICLE{Buze2021,
  title     = "Numerical-continuation-enhanced flexible boundary condition
               scheme applied to mode-I and {mode-III} fracture",
  author    = "Buze, Maciej and Kermode, James R",
  journal   = "Phys. Rev. E",
  publisher = "American Physical Society",
  volume    =  103,
  number    =  3,
  pages     = "033002",
  month     =  mar,
  year      =  2021,
  doi       = "10.1103/PhysRevE.103.033002"
}

@article{Martinez2009,
  title = {{{PACKMOL}}: {{A}} Package for Building Initial Configurations for Molecular Dynamics Simulations},
  author = {Martinez, L. and Andrade, R and Birgin, E G and Mart{\'i}nez, J M},
  year = {2009},
  journal = {Journal of Computational Chemistry},
  volume = {30},
  number = {13},
  pages = {2157--2164},
  issn = {01928651},
  doi = {10.1002/jcc.21224},
  abstract = {Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van derWaals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/{$\sim$}martinez/packmol/. \textcopyright},
  arxiv = {NIHMS150003},
  isbn = {1096-987X},
  pmid = {20928852},
  keywords = {initial configuration,MD,micelle},
  annotation = {02301},
}

@book{Selberherr1984,
  title = {Analysis and simulation of semiconductor devices},
  author = {Selberherr, Siegfried},
  year = {1984},
  publisher = {Springer Science \& Business Media},
  doi = {10.1007/978-3-7091-8752-4}
}

@article{Seidl2021,
  title = {Molecular Simulations of Electrotunable Lubrication: Viscosity and Wall Slip in Aqueous Electrolytes},
  author = {Seidl, Christian and H{\"o}rmann, Johannes L. and Pastewka, Lars},
  year = {2021},
  month = jan,
  journal = {Tribology Letters},
  volume = {69},
  number = {1},
  pages = {22},
  issn = {1573-2711},
  doi = {10.1007/s11249-020-01395-6},
  abstract = {We study the frictional response of water-lubricated gold electrodes subject to an electrostatic potential difference using molecular dynamics simulations. Contrary to previous studies on electrotunable lubrication that were carried out by fixing the charges, our simulations keep electrodes at fixed electrostatic potential using a variable charge method. For pure water and NaCl solutions, viscosity is independent of the polarization of the electrodes, but wall slip depends on the potential difference. Our findings are in agreement with previous analytical theories of how wall slip is affected by interatomic interactions. The simulations shed light on the role of electrode polarization for wall slip and illustrate a mechanism for controlling friction and nanoscale flow in simple aqueous lubricants.},
  langid = {english},
}

@article{Bazant2006,
  title = {Current-{{Voltage Relations}} for {{Electrochemical Thin Films}}},
  author = {Bazant, Martin Z. and Chu, Kevin T. and Bayly, B. J.},
  year = {2006},
  month = jul,
  journal = {SIAM Journal on Applied Mathematics},
  publisher = {{Society for Industrial and Applied Mathematics}},
  doi = {10.1137/040609938},
  abstract = {The DC response of an electrochemical thin film, such as the separator in a microbattery, is analyzed by solving the Poisson--Nernst--Planck equations, subject to boundary conditions appropriate fo...},
  copyright = {Copyright \textcopyright{} 2005 Society for Industrial and Applied Mathematics},
  langid = {english},
}

@ARTICLE{Jorgensen1996,
  title     = "Development and Testing of the OPLS All-Atom Force Field on
               Conformational Energetics and Properties of Organic Liquids",
  author    = "Jorgensen, William L. and Maxwell, David S. and
               Tirado-Rives, Julian",
  journal   = "Journal of the American Chemical Society",
  volume    =  118,
  number    =  45,
  pages     = "11225-11236",
  year      =  1996,
  doi       = "10.1021/ja9621760"
}

@ARTICLE{Thompson2022,
  title     = "LAMMPS - a flexible simulation tool for particle-based
               materials modeling at the atomic, meso, and continuum scale",
  author    = "Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard
               and Bolintineanu, Dan S. and Brown, W. Michael and
               Crozier, Paul S. and {in 't Veld}, Pieter J. and Kohlmeyer, Axel
               and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and
               Stevens, Mark J. and Tranchida, Julien and Trott, Christian
               and Plimpton, Steven J.",
  journal   = "Computer Physics Communications",
  volume    =  271,
  pages     = "108171",
  year      =  2022,
  doi       = "10.1016/j.cpc.2021.108171"
}

@ARTICLE{Mayrhofer2016,
  title     = "Fluorine-Terminated Diamond Surfaces as Dense Dipole Lattices:
               The Electrostatic Origin of Polar Hydrophobicity",
  author    = "Mayrhofer, Leonhard and Moras, Gianpietro and
               Mulakaluri, Narasimham and Rajagopalan, Srinivasan and
               Stevens, Paul A. and Moseler, Michael",
  journal   = "Journal of the American Chemical Society",
  volume    =  138,
  pages     = "4018-4028",
  year      =  2016,
  doi       = "10.1021/jacs.5b04073"
}

@ARTICLE{Falk2020,
  title     = "Nonempirical Free Volume Viscosity Model for Alkane Lubricants
               under Severe Pressures",
  author    = "Falk, Kerstin and Savio, Daniele and Moseler, Michael",
  journal   = "Phys. Rev. Lett.",
  volume    =  124,
  pages     = "105501",
  year      =  2020,
  doi       = "10.1103/PhysRevLett.124.105501"
}

@ARTICLE{Reichenbach2020,
  title     = "Steric Effects Control Dry Friction of H- and F-Terminated
               Carbon Surfaces",
  author    = "Reichenbach, Thomas and Mayrhofer, Leonhard and
               Kuwahara, Takuya and Moseler, Michael and Moras, Gianpietro",
  journal   = "ACS Applied Materials \& Interfaces",
  volume    =  12,
  pages     = "8805-8816",
  year      =  2020,
  doi       = "10.1021/acsami.9b18019"
}

@ARTICLE{vonGoeldel2021,
  title     = "A Combined Experimental and Atomistic Investigation of PTFE
               Double Transfer Film Formation and Lubrication in Rolling
               Point Contacts",
  author    = "von Goeldel, Stephan and Reichenbach, Thomas and
               Konig, Florian and Mayrhofer, Leonhard and
               Moras, Gianpietro and Jacobs, Georg and
               Moseler, Michael",
  journal   = "Tribology Letters",
  volume    =  69,
  pages     = "136",
  year      =  2021,
  doi       = "10.1007/s11249-021-01508-9"
}

@ARTICLE{Falk2022,
  title     = "Relating Dry Friction to Interdigitation of Surface
               Passivation Species: A Molecular Dynamics Study on Amorphous
               Carbon",
  author    = "Falk, Kerstin and Reichenbach, Thomas and Gkagkas, Konstantinos
               and Moseler, Michael and Moras, Gianpietro",
  journal   = "Materials",
  volume    =  15,
  number    =  9,
  pages     = "3247",
  year      =  2022,
  doi       = "10.3390/ma15093247"
}

@book{LoggMardalEtAl2012,
  title = {Automated Solution of Differential Equations by the Finite Element Method},
  author = {Anders Logg and Kent-Andre Mardal and Garth N. Wells and others},
  editor = {Anders Logg and Kent-Andre Mardal and Garth N. Wells},
  year = {2012},
  publisher = {Springer},
  doi = {10.1007/978-3-642-23099-8},
  isbn = {978-3-642-23098-1},
}

@ARTICLE{Griesser2023glass,
  title     = "Yielding under compression and the polyamorphic transition in
               silicon",
  author    = "Grie{\ss}er, Jan and Moras, Gianpietro and Pastewka, Lars",
  journal   = "Phys. Rev. Mater.",
  publisher = "American Physical Society",
  volume    =  7,
  number    =  5,
  pages     = "055601",
  month     =  may,
  year      =  2023,
  doi       = "10.1103/PhysRevMaterials.7.055601"
}

@ARTICLE{Griesser2023crystal,
  title         = "Analytic elastic constants in molecular calculations: Finite
                   strain, non-affine displacements, and many-body interatomic
                   potentials",
  author        = "Grie{\ss}er, Jan and Fr{\'e}rot, Lucas and Oldenstaedt,
                   Jonas A and M{\"u}ser, Martin H and Pastewka, Lars",
  abstract      = "Elastic constants are among the most fundamental and
                   important properties of solid materials, which is why they
                   are routinely characterized in both experiments and
                   simulations. While conceptually simple, the treatment of
                   elastic constants is complicated by two factors not yet
                   having been concurrently discussed: finite-strain and
                   non-affine, internal displacements. Here, we revisit the
                   theory behind zero-temperature, finite-strain elastic
                   constants and extend it to explicitly consider non-affine
                   displacements. We further present analytical expressions for
                   second-order derivatives of the potential energy for
                   two-body and generic many-body interatomic potentials, such
                   as cluster and empirical bond-order potentials.
                   Specifically, we revisit the elastic constants of silicon,
                   silicon carbide and silicon dioxide under hydrostatic
                   compression and dilatation. Based on existing and new
                   results, we outline the effect of multiaxial stress states
                   as opposed to volumetric deformation on the limits of
                   stability of their crystalline lattices.",
  year          =  2023,
  journal       = "Phys. Rev. Mater.",
  volume        = 7,
  number        = 7,
  pages         = "073603",
  doi           = "10.1103/PhysRevMaterials.7.073603"
}

@ARTICLE{Miller2009,
  title   = "A unified framework and performance benchmark of fourteen
             multiscale atomistic/continuum coupling methods",
  author  = "Miller, Ronald E and Tadmor, Ellad B",
  journal = "Modell. Simul. Mater. Sci. Eng.",
  volume  =  17,
  number  =  5,
  pages   = "053001",
  month   =  jul,
  year    =  2009,
  doi     =  "10.1088/0965-0393/17/5/053001"
}

@ARTICLE{Anciaux2018,
  title    = "The Coupled {Atomistic/Discrete-Dislocation} method in 3d part I:
              Concept and algorithms",
  author   = "Anciaux, G and Junge, T and Hodapp, M and Cho, J and Molinari,
              J-F and Curtin, W A",
  abstract = "The Coupled Atomistic/Discrete-Dislocation (CADD) method is a
              concurrent multiscale technique that couples atomistic and
              discrete dislocation domains with the ability to pass
              dislocations seamlessly between domains. CADD has been
              demonstrated only in 2d plane-strain problems, for which each
              individual dislocation is either entirely atomistic or entirely
              discrete. Here, a full 3d implementation of CADD is presented,
              with emphasis on the algorithms for handling the description of
              dislocation lines that span both atomistic and continuum domains,
              so-called hybrid dislocations. The key new features of the method
              for 3d are (i) the use of an atomistic template of the
              dislocation core structure to transmit the proper atomistic
              environment of a continuum dislocation to the atomistic domain
              for hybrid dislocations and (ii) a staggered solution procedure
              enabling evolution of the hybrid dislocations. The method
              naturally requires calibration of discrete-dislocation Peierls
              stresses and mobilities to their atomistic values, implementation
              of a dislocation detection algorithm to identify atomistic
              dislocations, and computation of continuum dislocation
              displacement fields that provide boundary conditions for the
              atomistic problem. The method is implemented using the atomistic
              code LAMMPS and the discrete dislocation code ParaDiS within the
              LibMultiscale environment developed by the lead authors, and so
              has all the advantages of these widely-used high-performance
              open-source codes. Validation and application of CADD-3d are
              presented in companion papers.",
  journal  = "J. Mech. Phys. Solids",
  volume   =  118,
  pages    = "152--171",
  month    =  sep,
  year     =  2018,
  doi      =  "10.1016/j.jmps.2018.05.004"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Anciaux2007,
  title     = "Simulation multi-{\'e}chelles des solides par une approche
               coupl{\'e}e dynamique mol{\'e}culaire/{\'e}l{\'e}ments finis. De
               la mod{\'e}lisation {\`a} la simulation haute performance",
  author    = "Anciaux, G",
  abstract  = "Cette th{\`e}se porte sur l'{\'e}tude de la simulation des
               solides par des m{\'e}thodes de couplage multi-{\'e}chelles
               (m{\'e}thode atomique/continue ACM). Dans ce travail de
               th{\`e}se, nous abordons …",
  publisher = "theses.hal.science",
  year      =  2007
}

@ARTICLE{Campana2006,
  title   = "Practical Green's function approach to the simulation of elastic
             semi-infinite solids",
  author  = "Campa{\~n}{\'a}, Carlos and M{\"u}ser, Martin H",
  journal = "Phys. Rev. B",
  volume  =  74,
  number  =  7,
  pages   = "075420",
  year    =  2006,
  doi     = "10.1103/PhysRevB.74.075420"
}

@ARTICLE{Pastewka2012,
  title   = "Seamless elastic boundaries for atomistic calculations",
  author  = "Pastewka, Lars and Sharp, Tristan A and Robbins, Mark O",
  journal = "Phys. Rev. B",
  volume  =  86,
  pages   = "075459",
  year    =  2012,
  doi     = "10.1103/PhysRevB.86.075459"
}

@ARTICLE{Falk1998,
  title    = "Dynamics of viscoplastic deformation in amorphous solids",
  author   = "Falk, Michael L and Langer, J S",
  abstract = "for situations in which the stresses necessarily rise to values
              at or 7204 AND 45 . Carlson and A. Batista, 46 S. and A. Liu
              unpublished",
  journal  = "Phys. Rev. E",
  volume   =  57,
  number   =  6,
  pages    = "7192--7205",
  month    =  jun,
  year     =  1998,
  doi      = "10.1103/PhysRevE.57.7192"
}

@ARTICLE{Jana2019,
  title    = "Correlations of non-affine displacements in metallic glasses
              through the yield transition",
  author   = "Jana, Richard and Pastewka, Lars",
  abstract = "We study correlations of non-affine displacements during simple
              shear deformation of Cu--Zr bulk metallic glasses in molecular
              dynamics calculations. In the elastic regime, our calculations
              show exponential correlation with a decay length that we
              interpret as the size of a shear transformation zone in the
              elastic regime. This correlation length becomes system-size
              dependent beyond the yield transition as our calculation develops
              a shear band, indicative of a diverging length scale. We discuss
              these observations in the context of a recent proposition of
              yield as a first-order phase transition.",
  journal  = "J. Phys. Mater.",
  volume   =  2,
  pages    = "045006",
  month    =  jul,
  year     =  2019,
  language = "en",
  doi      = "10.1088/2515-7639/ab36ed"
}

@ARTICLE{Gola2019,
  title    = "Surface flaws control strain localization in the deformation of
              {Cu|Au} nanolaminate pillars",
  author   = "Gola, Adrien and Zhang, Guang-Ping and Pastewka, Lars and
              Schwaiger, Ruth",
  abstract = ", The authors carried out matched experiments and molecular
              dynamics simulations of the compression of nanopillars prepared
              from Cu|Au nanolaminates with up to 25 nm layer thickness. The
              stress--strain behaviors obtained from both techniques are in
              excellent agreement. Variation in the layer thickness reveals an
              increase in the strength with a decreasing layer thickness.
              Pillars fail through the formation of shear bands whose
              nucleation they trace back to the existence of surface flaws.
              This combined approach demonstrates the crucial role of contact
              geometry in controlling the deformation mode and suggests that
              modulus-matched nanolaminates should be able to suppress strain
              localization while maintaining controllable strength.",
  journal  = "MRS Communications",
  volume   =  9,
  number   =  3,
  pages    = "1067--1071",
  year     =  2019,
  language = "en",
  doi      = "10.1557/mrc.2019.93"
}

@ARTICLE{Gola2020,
  title    = "Pattern formation during deformation of metallic nanolaminates",
  author   = "Gola, Adrien and Schwaiger, Ruth and Gumbsch, Peter and Pastewka,
              Lars",
  abstract = "We used nonequilibrium molecular dynamics simulations to study
              the shear deformation of metallic composites composed of
              alternating layers of Cu and Au. Our simulations reveal the
              formation of ``vortices'' or ``swirls'' if the bimaterial
              interfaces are atomically rough and if none of the \{111\} planes
              that accommodate slip in fcc materials are exactly parallel to
              this interface. We trace the formation of these patterns back to
              grain rotation, induced by hindering dislocations from crossing
              the bimaterial interface. The instability is accompanied by shear
              softening of the material. These calculations shed light on
              recent observations of pattern formation in plastic flow,
              mechanical mixing of materials, and the common formation of a
              tribomutation layer in tribologically loaded systems.",
  journal  = "Phys. Rev. Mater.",
  volume   =  4,
  number   =  1,
  pages    = "013603",
  month    =  jan,
  year     =  2020,
  doi      = "10.1103/PhysRevMaterials.4.013603"
}

@ARTICLE{Franzblau1991,
  title   = "Computation of ring statistics for network models of solids",
  author  = "Franzblau, Deborah S",
  journal = "Phys. Rev. B",
  volume  =  44,
  number  =  10,
  pages   = "4925--4930",
  month   =  sep,
  year    =  1991,
  doi     = "10.1103/PhysRevB.44.4925"
}

@TECHREPORT{Saad1990,
  title     = "{SPARSKIT}: A basic tool kit for sparse matrix computations",
  author    = "Saad, Youcef",
  abstract  = "Presented here are the main features of a tool package for
               manipulating and working with sparse matrices. One of the goals
               of the package is to provide basic tools to facilitate the
               exchange of software and data between researchers in sparse
               matrix computations. The starting point is the Harwell/Boeing
               collection of matrices for which the authors provide a number of
               tools. Among other things, the package provides programs for
               converting data structures, printing simple statistics on a
               matrix, plotting a matrix profile, and performing linear algebra
               operations with sparse matrices.",
  publisher = "ntrs.nasa.gov",
  number    = "NAS 1.26:185876",
  month     =  may,
  year      =  1990
}

@ARTICLE{Pastewka2008,
  title   = "Describing bond-breaking processes by reactive potentials:
             Importance of an environment-dependent interaction range",
  author  = "Pastewka, Lars and Pou, Pablo and P{\'e}rez, Rub{\'e}n and
             Gumbsch, Peter and Moseler, Michael",
  journal = "Phys. Rev. B Condens. Matter",
  volume  =  78,
  number  =  16,
  pages   = "161402(R)",
  year    =  2008,
  doi     = "10.1103/PhysRevB.78.161402"
}

@ARTICLE{Jana2019,
  title    = "Structural and elastic properties of amorphous carbon from
              simulated quenching at low rates",
  author   = "Jana, Richard and Savio, Daniele and Deringer, Volker and
              Pastewka, Lars",
  abstract = "We generate representative structural models of amorphous carbon
              (a-C) from constant-volume quenching from the liquid with
              subsequent relaxation of internal stresses in molecular dynamics
              simulations using empirical and machine-learning interatomic
              potentials. By varying volume and quench rate we generate
              structures with a range of density and amorphous morphologies. We
              find that all a-C samples show a universal relationship between
              hybridization, bulk modulus and density despite having distinctly
              different cohesive energies. Differences in cohesive energy are
              traced back to slight changes in the distribution of bond-angles
              that will likely be linked to thermal stability of these
              structures.",
  journal  = "Modell. Simul. Mater. Sci. Eng.",
  volume   =  27,
  pages    = "085009",
  year     =  2019,
  language = "en",
  doi      = "10.1088/1361-651X/ab45da"
}

@ARTICLE{Muser2023,
  title     = "Interatomic potentials: achievements and challenges",
  author    = "M{\"u}ser, Martin H and Sukhomlinov, Sergey V and Pastewka, Lars",
  abstract  = "ABSTRACTInteratomic potentials approximate the potential energy
               of atoms as a function of their coordinates. Their main
               application is the effective simulation of many-atom systems.
               Here, we review empirical interatomic potentials designed to
               reproduce elastic properties, defect energies, bond breaking,
               bond formation, and even redox reactions. We discuss popular
               two-body potentials, embedded-atom models for metals, bond-order
               potentials for covalently bonded systems, polarizable potentials
               including charge-transfer approaches for ionic systems and
               quantum-Drude oscillator models mimicking higher-order and
               many-body dispersion. Particular emphasis is laid on the
               question what constraints ensue from the functional form of a
               potential, e.g., in what way Cauchy relations for elastic tensor
               elements can be violated and what this entails for the ratio of
               defect and cohesive energies, or why the ratio of boiling to
               melting temperature tends to be large for potentials describing
               metals but small for short-ranged pair potentials. The review is
               meant to be pedagogical rather than encyclopedic. This is why we
               highlight potentials with functional forms sufficiently simple
               to remain amenable to analytical treatments. Our main objective
               is to provide a stimulus for how existing approaches can be
               advanced or meaningfully combined to extent the scope of
               simulations based on empirical potentials.",
  journal   = "Advances in Physics: X",
  publisher = "Taylor \& Francis",
  volume    =  8,
  number    =  1,
  pages     = "2093129",
  month     =  jan,
  year      =  2023,
  doi       = "10.1080/23746149.2022.2093129"
}

@inproceedings{
Batatia2022mace,
title={{MACE}: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields},
author={Ilyes Batatia and David Peter Kovacs and Gregor N. C. Simm and Christoph Ortner and Gabor Csanyi},
booktitle={Advances in Neural Information Processing Systems},
editor={Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho},
year={2022},
url={https://openreview.net/forum?id=YPpSngE-ZU}
}

@misc{Batatia2022Design,
  title = {The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials},
  author = {Batatia, Ilyes and Batzner, Simon and Kov{\'a}cs, D{\'a}vid P{\'e}ter and Musaelian, Albert and Simm, Gregor N. C. and Drautz, Ralf and Ortner, Christoph and Kozinsky, Boris and Cs{\'a}nyi, G{\'a}bor},
  year = {2022},
  number = {arXiv:2205.06643},
  eprint = {2205.06643},
  eprinttype = {arxiv},
  doi = {10.48550/arXiv.2205.06643},
  archiveprefix = {arXiv}
 }

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Peguiron2016-wf,
  title   = "Activation and mechanochemical breaking of {C−C} bonds initiate
             wear of diamond (110) surfaces in contact with silica",
  author  = "Peguiron, Anke and Moras, Gianpietro and Walter, Michael and
             Uetsuka, Hiroshi and Pastewka, Lars and Moseler, Michael",
  journal = "Carbon N. Y.",
  volume  =  98,
  pages   = "474--483",
  year    =  2016,
  doi     = "10.1016/j.carbon.2015.10.098"
}

@ARTICLE{Moras2018-lm,
  title   = "Shear melting of silicon and diamond and the disappearance of the
             polyamorphic transition under shear",
  author  = "Moras, Gianpietro and Klemenz, Andreas and Reichenbach, Thomas and
             Gola, Adrien and Uetsuka, Hiroshi and Moseler, Michael and
             Pastewka, Lars",
  journal = "Phys. Rev. Materials",
  volume  =  2,
  number  =  8,
  pages   = "083601",
  month   =  aug,
  year    =  2018,
  doi     = "10.1103/PhysRevMaterials.2.083601"
}

@ARTICLE{Reichenbach2021-pi,
  title    = "Solid-Phase Silicon Homoepitaxy via Shear-Induced
              Amorphization and Recrystallization",
  author   = "Reichenbach, Thomas and Moras, Gianpietro and Pastewka, Lars and
              Moseler, Michael",
  abstract = "We study mechanically induced phase transitions at tribological
              interfaces between silicon crystals using reactive molecular
              dynamics. The simulations reveal that the interplay between
              shear-driven amorphization and recrystallization results in an
              amorphous shear interface with constant thickness. Different
              shear elastic responses of the two anisotropic crystals can lead
              to the migration of the amorphous interface normal to the sliding
              plane, causing the crystal with lowest elastic energy density to
              grow at the expense of the other one. This triboepitaxial growth
              can be achieved by crystal misorientation or exploiting elastic
              finite-size effects, enabling the direct deposition of
              homoepitaxial silicon nanofilms by a crystalline tip rubbing
              against a substrate.",
  journal  = "Phys. Rev. Lett.",
  volume   =  127,
  number   =  12,
  pages    = "126101",
  month    =  sep,
  year     =  2021,
  language = "en",
  doi      = "10.1103/PhysRevLett.127.126101"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Moras2011-my,
  title     = "Formation and oxidation of linear carbon chains and their role
               in the wear of carbon materials",
  author    = "Moras, G and Pastewka, L and Gumbsch, P and Moseler, M",
  abstract  = "The atomic-scale processes taking place during the sliding of
               diamond and diamond-like carbon surfaces are investigated using
               classical molecular dynamics simulations. During the …",
  journal   = "Tribol. Lett.",
  publisher = "Springer",
  year      =  2011,
  doi       = "10.1007/s11249-011-9864-9"
}

@ARTICLE{Pastewka2011-rd,
  title   = "Anisotropic mechanical amorphization drives wear in diamond",
  author  = "Pastewka, Lars and Moser, Stefan and Gumbsch, Peter and Moseler,
             Michael",
  journal = "Nat. Mater.",
  volume  =  10,
  number  =  1,
  pages   = "34--38",
  month   =  nov,
  year    =  2011,
  doi     = "10.1038/nmat2902"
}

@ARTICLE{Hormann2023-ml,
  title    = "Molecular simulations of sliding on {SDS} surfactant films",
  author   = "H{\"o}rmann, Johannes L and Liu, Chenxu and Meng, Yonggang and
              Pastewka, Lars",
  abstract = "We use molecular dynamics simulations to study the frictional
              response of monolayers of the anionic surfactant sodium dodecyl
              sulfate and hemicylindrical aggregates physisorbed on gold. Our
              simulations of a sliding spherical asperity reveal the following
              two friction regimes: at low loads, the films show Amonton's
              friction with a friction force that rises linearly with normal
              load, and at high loads, the friction force is independent of the
              load as long as no direct solid-solid contact occurs. The
              transition between these two regimes happens when a single
              molecular layer is confined in the gap between the sliding
              bodies. The friction force at high loads on a monolayer rises
              monotonically with film density and drops slightly with the
              transition to hemicylindrical aggregates. This monotonous
              increase of friction force is compatible with a traditional
              plowing model of sliding friction. At low loads, the friction
              coefficient reaches a minimum at the intermediate surface
              concentrations. We attribute this behavior to a competition
              between adhesive forces, repulsion of the compressed film, and
              the onset of plowing.",
  journal  = "J. Chem. Phys.",
  volume   =  158,
  number   =  24,
  month    =  jun,
  year     =  2023,
  language = "en",
  doi      = "10.1063/5.0153397"
}

@ARTICLE{Harris2020-it,
  title    = "Array programming with {NumPy}",
  author   = "Harris, Charles R and Millman, K Jarrod and van der Walt,
              St{\'e}fan J and Gommers, Ralf and Virtanen, Pauli and
              Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg,
              Sebastian and Smith, Nathaniel J and Kern, Robert and Picus,
              Matti and Hoyer, Stephan and van Kerkwijk, Marten H and Brett,
              Matthew and Haldane, Allan and del R{\'\i}o, Jaime Fern{\'a}ndez
              and Wiebe, Mark and Peterson, Pearu and G{\'e}rard-Marchant,
              Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren
              and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E",
  abstract = "Array programming provides a powerful, compact and expressive
              syntax for accessing, manipulating and operating on data in
              vectors, matrices and higher-dimensional arrays. NumPy is the
              primary array programming library for the Python language. It has
              an essential role in research analysis pipelines in fields as
              diverse as physics, chemistry, astronomy, geoscience, biology,
              psychology, materials science, engineering, finance and
              economics. For example, in astronomy, NumPy was an important part
              of the software stack used in the discovery of gravitational
              waves1 and in the first imaging of a black hole2. Here we review
              how a few fundamental array concepts lead to a simple and
              powerful programming paradigm for organizing, exploring and
              analysing scientific data. NumPy is the foundation upon which the
              scientific Python ecosystem is constructed. It is so pervasive
              that several projects, targeting audiences with specialized
              needs, have developed their own NumPy-like interfaces and array
              objects. Owing to its central position in the ecosystem, NumPy
              increasingly acts as an interoperability layer between such array
              computation libraries and, together with its application
              programming interface (API), provides a flexible framework to
              support the next decade of scientific and industrial analysis.",
  journal  = "Nature",
  volume   =  585,
  number   =  7825,
  pages    = "357--362",
  month    =  sep,
  year     =  2020,
  language = "en",
  doi      = "10.1038/s41586-020-2649-2"
}

@ARTICLE{Virtanen2020-tq,
  title    = "{SciPy} 1.0: fundamental algorithms for scientific computing in
              Python",
  author   = "Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E and
              Haberland, Matt and Reddy, Tyler and Cournapeau, David and
              Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
              Bright, Jonathan and van der Walt, St{\'e}fan J and Brett,
              Matthew and Wilson, Joshua and Millman, K Jarrod and Mayorov,
              Nikolay and Nelson, Andrew R J and Jones, Eric and Kern, Robert
              and Larson, Eric and Carey, C J and Polat, {\.I}lhan and Feng, Yu
              and Moore, Eric W and VanderPlas, Jake and Laxalde, Denis and
              Perktold, Josef and Cimrman, Robert and Henriksen, Ian and
              Quintero, E A and Harris, Charles R and Archibald, Anne M and
              Ribeiro, Ant{\^o}nio H and Pedregosa, Fabian and van Mulbregt,
              Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and
              Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll,
              Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee,
              Antony and Rokem, Ariel and Woods, C Nathan and Fulton, Chad and
              Masson, Charles and H{\"a}ggstr{\"o}m, Christian and Fitzgerald,
              Clark and Nicholson, David A and Hagen, David R and Pasechnik,
              Dmitrii V and Olivetti, Emanuele and Martin, Eric and Wieser,
              Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian
              and Young, G and Price, Gavin A and Ingold, Gert-Ludwig and
              Allen, Gregory E and Lee, Gregory R and Audren, Herv{\'e} and
              Probst, Irvin and Dietrich, J{\"o}rg P and Silterra, Jacob and
              Webber, James T and Slavi{\v c}, Janko and Nothman, Joel and
              Buchner, Johannes and Kulick, Johannes and Sch{\"o}nberger,
              Johannes L and de Miranda Cardoso, Jos{\'e} Vin{\'\i}cius and
              Reimer, Joscha and Harrington, Joseph and Rodr{\'\i}guez, Juan
              Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and
              Tritz, Kevin and Thoma, Martin and Newville, Matthew and
              K{\"u}mmerer, Matthias and Bolingbroke, Maximilian and Tartre,
              Michael and Pak, Mikhail and Smith, Nathaniel J and Nowaczyk,
              Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and
              Brodtkorb, Per A and Lee, Perry and McGibbon, Robert T and
              Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert,
              Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud
              and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J and
              Robitaille, Thomas P and Spura, Thomas and Jones, Thouis R and
              Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and
              Upadhyay, Utkarsh and Halchenko, Yaroslav O and
              V{\'a}zquez-Baeza, Yoshiki",
  abstract = "Abstract SciPy is an open-source scientific computing library for
              the Python programming language. Since its initial release in
              2001, SciPy has become a de facto standard for leveraging
              scientific algorithms in Python, with over 600 unique code
              contributors, thousands of dependent packages, over 100,000
              dependent repositories and millions of downloads per year. In
              this work, we provide an overview of the capabilities and
              development practices of SciPy 1.0 and highlight some recent
              technical developments.",
  journal  = "Nat. Methods",
  volume   =  17,
  number   =  3,
  pages    = "261--272",
  month    =  mar,
  year     =  2020,
  language = "en",
  doi      = "10.1038/s41592-019-0686-2"
}

@ARTICLE{Hirel2015-ts,
  title    = "Atomsk: A tool for manipulating and converting atomic data files",
  author   = "Hirel, Pierre",
  abstract = "We present a libre, Open Source command-line program named
              Atomsk, that aims at creating and manipulating atomic systems for
              the purposes of ab initio calculations, classical atomistic
              calculations, and visualization, in the areas of computational
              physics and chemistry. The program can run on GNU/Linux, Apple
              Mac OS X, and Microsoft Windows platforms. Many file formats are
              supported, allowing for easy conversion of atomic configuration
              files. The command-line options allow to construct supercells,
              insert point defects (vacancies, interstitials), line defects
              (dislocations, cracks), plane defects (stacking faults), as well
              as other transformations. Several options can be applied
              consecutively, allowing for a comprehensive workflow from a unit
              cell to the final atomic system. Some modes allow to construct
              complex structures, or to perform specific analysis of atomic
              systems. Program summary Program title: Atomsk Catalogue
              identifier: AEXM\_v1\_0 Program summary
              URL:http://cpc.cs.qub.ac.uk/summaries/AEXM\_v1\_0.html Program
              obtainable from: CPC Program Library, Queen's University,
              Belfast, N. Ireland Licensing provisions: GNU/GPL version 3 or
              any later version No. of lines in distributed program, including
              test data, etc.: 61,450 No. of bytes in distributed program,
              including test data, etc.: 539,898 Distribution format: tar.gz
              Programming language: Fortran 90. Computer: All computers with a
              Fortran compiler supporting at least Fortran 90. Operating
              system: All operating systems with such a compiler. Some of the
              Makefiles and scripts depend on a Unix-like system and need
              modification under Windows. RAM: Typically 32 bytes $\times$ N,
              where N is the number of particles. Classification: 4.14, 7.1.
              External routines: LAPACK Nature of problem: Atomistic
              simulations require the generation of atomic data files. Few
              software are available to construct atomic systems containing
              dislocations, especially in anisotropic media. Solution method:
              Atomsk is a unified program that allows to generate, convert and
              transform atomic systems for the purposes of ab initio
              calculations, classical atomistic simulations, or visualization.
              It supports many lattice types, all atom chemical species, and
              supports systems described with the ionic core--shell model. It
              allows to construct dislocations and analyze them, and perform
              post-treatment of simulation output files. Restrictions: no
              support for molecular bonds; limit of 2 billions particles.
              Unusual features: dislocations in anisotropic media; computation
              of the Nye tensor; generation of polycrystal from any type of
              lattice; support for ionic core--shell models and analysis of
              electric polarization. Additional comments: the program and its
              documentation are available at: http://atomsk.univ-lille1.fr
              Running time: spans from a fraction of a second to several
              minutes depending on the number of particles in the atomic
              system, the mode, and the machine performance.",
  journal  = "Comput. Phys. Commun.",
  volume   =  197,
  pages    = "212--219",
  month    =  dec,
  year     =  2015,
  doi      = "10.1016/j.cpc.2015.07.012"
}

@article{Daw1984,
  title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
  author = {Daw, Murray S. and Baskes, Michael I.},
  journal = {Physical Review B},
  volume = {29},
  issue = {12},
  pages = {6443--6453},
  numpages = {0},
  year = {1984},
  month = {Jun},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.29.6443},
  url = {https://link.aps.org/doi/10.1103/PhysRevB.29.6443}
}

@article{preCICEv2,
  author = {Chourdakis, G and Davis, K and Rodenberg, B and Schulte, M and Simonis, F and Uekermann, B and Abrams, G and Bungartz, HJ and Cheung Yau, L and Desai, I and Eder, K and Hertrich, R and Lindner, F and Rusch, A and Sashko, D and Schneider, D and Totounferoush, A and Volland, D and Vollmer, P and Koseomur, OZ},
  title = {{preCICE} v2: A sustainable and user-friendly coupling library [version 2; peer review: 2 approved]
  },
  journal = {Open Research Europe},
  volume = {2},
  year = {2022},
  number = {51},
  doi = {10.12688/openreseurope.14445.2},
  url = {https://doi.org/10.12688/openreseurope.14445.2}
}

@InProceedings{Dehning2014,
author="Dehning, Carsten
and Bierwisch, Claas
and Kraft, Torsten",
editor="Griebel, Michael
and Schweitzer, Marc Alexander",
title="Co-simulations of Discrete and Finite Element Codes",
booktitle="Meshfree Methods for Partial Differential Equations VII",
year="2015",
publisher="Springer International Publishing",
address="Cham",
pages="61--79",
abstract="This paper describes methods and algorithms implemented for the co-simulation between a mesh-free discrete element method (DEM) code and a finite element analysis (FEA) code under control of a co-simulation middleware software environment.",
isbn="978-3-319-06898-5"
}
